[ccp4bb] Announcement: Standardization of Amino Acid Nomenclature

Announcement: Standardization of Amino Acid Nomenclature The wwPDB is transitioning to use the nomenclature for pyrrolysine and selenocysteine as recommended by the joint nomenclature committee of IUPAC/IUBMB. Starting in January, PYL (for pyrrolysine) and SEC (for selenocysteine) will be

Re: [ccp4bb] Question: Refmac5 stats reported in pdb REMARK 3

between our PDB Exchange Data Dictionary and items in the current PDB format is also available at http://mmcif.pdb.org/dictionaries/pdb-correspondence/pdb2mmcif-2010.html Sincerely, Christine Zardecki for the wwPDB From: Phil Jeffrey pjeff...@princeton.edu Date: May 19, 2010 4:02:22 PM EDT

Re: [ccp4bb] Finding best model for molecular replacement

Dear Paul, A few options may be of interest: RCSB PDB Sequence Searching: Paste your sequence into the sequence search box at: http://www.pdb.org/pdb/search/advSearch.do?st=SequenceQuery (also available from Advanced Search and from the Sequence Search of the left hand menu). Sequence

Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot

Hello, The CIFTr program is a simplied mmCIF to PDB format converter that can be downloaded at http://sw-tools.pdb.org/apps/CIFTr/index.html. A more complete conversion, including remarks and other experimental details, can be performed using the Maxit program. This program can be downloaded

[ccp4bb] Where to find novelty of PDBids?

TargetDB performs this type of analysis for structures deposited by structural genomics projects. Tabulations of novel depositions can be found at http://targetdb.pdb.org/Metrics/MilestonesTables.html. The data from which these statistics were calculated from sequence clustering performed

[ccp4bb] Improved Version of ADIT Available

Improved Version of ADIT Available An updated and enhanced version of ADIT is now available for depositing new entries at http://deposit-beta.rcsb.org/adit/. We encourage depositors to use this new tool and send feedback to depo...@deposit.rcsb.org. ADIT is used to validate and submit

Re: [ccp4bb] LIGPLOT or similar

Mark, Ligand Explorer displays hydrogen bonds, water-mediated hydrogen bonds, metal coordination, and hydrophobic contacts. High resolution images can be exported in several file formats. Ligand Explorer is available from each PDB entry's Structure Summary page at the RCSB PDB

[ccp4bb] Due Aug 1: PDB40 Travel Award Applications for Early Career Scientists and Students

Celebrate four decades of innovation in structural biology this fall at a Cold Spring Harbor Laboratory symposium honoring the PDB's 40th anniversary and the many scientific contributions it archives. TRAVEL AWARDS Limited funds are available to help students and early career scientists attend

Re: [ccp4bb] Another paper structure retracted

://www.nature.com/nsmb/journal/v17/n8/full/nsmb0810-917.html). Christine Zardecki for the wwPDB -- PDB 40: Celebrate four decades of innovation in structural biology Oct 28-30, 2011 at Cold Spring Harbor Laboratory http

Re: [ccp4bb] _diffrn.detail in PDB sf.cif releases

This is an error that will be corrected; we'll also fix the source of the problem so that it won't appear again. Thanks to Tom Womack for bringing this to our attention. Questions and comments for the wwPDB about data files and formats may also be sent i...@wwpdb.org. Christine for the

[ccp4bb] wwPDB Announcements: Validation Report PDFs, NMR Restraint Files

wwPDB To Provide Validation Reports as PDFs As part of the structure annotation process, wwPDB members provide depositors with detailed reports that include the results of geometric and experimental data checking. Beginning May 17, 2010, these documents will be available from all wwPDB

Re: [ccp4bb] 3D printing format

The NIH 3D Print Exchange (http://3dprint.nih.gov/) has a collection of files for 3D printing, and can generate files based on PDB ID. Christine -- Twitter: http://twitter.com/#!/buildmodels Facebook:

[ccp4bb] Scientific Software Developer position at RCSB Protein Data Bank (RCSB.org) at the University of California San Diego (UCSD)

For contact information and other positions, please see http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/contact/job_listings.html Scientific Software Developer Develop, implement,

[ccp4bb] RCSB PDB looking for Postdoctoral Fellows to join our multidisciplinary development team at UC San Diego

The Challenge: Develop innovative analysis, integration, query, and visualization tools for 3D biomolecular structures to help accelerate research and training in biology, medicine, and related disciplines. In these projects, we employ the latest advances in computer science to develop highly

[ccp4bb] Please Respond to the RCSB PDB User Survey and Raffle

RCSB PDB is running an online survey to help us better understand RCSB.org and PDB-101 users and interests. People who submit their responses at https://www.surveymonkey.com/r/RLRGRXX can also enter into a drawing for a poster, 2018 calendar, or Zika model. All users are encouraged to respond.

[ccp4bb] Beta Test the Next Generation RCSB PDB website at http://beta.rcsb.org

of each page. ------ CHRISTINE ZARDECKI Deputy Director, RCSB Protein Data Bank Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 P: 848.

[ccp4bb] Celebrate PDB50 at the Inaugural May 4-5 Event (Early Registration and Poster Abstracts by March 15)

Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB archive (http://wwpdb.org/pdb50 ). The inaugural symposium will be held virtually on May 4-5, 2021. The online sessions will take place between 11 a.m. – 4:30 p.m. ET each day. The event

[ccp4bb] Celebrate PDB50 at the Inaugural May 4-5 Event (register by March 15)

Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB archive (http://wwpdb.org/pdb50). The inaugural symposium will be held virtually on May 4-5, 2021. The online sessions will take place between 11 a.m. – 4:30 p.m. ET each day. The event will be recorded and made

[ccp4bb] User Survey: Tell RCSB PDB About Your Interests

RCSB PDB wants to learn more about our user. Please take this brief survey and be entered into a drawing for PDB50 Structural Biology Playing Cards: https://www.surveymonkey.com/r/65WVGB7 The results of this survey will help us better understand

[ccp4bb] Obituary for John D. Westbrook

John D. Westbrook Jr. (1957-2021), Research Professor at Rutgers University and Data & Software Architect Lead for the RCSB PDB, passed away on October 18, 2021. He was incredibly beloved and respected by his colleagues at Rutgers and throughout the world, known for his dry wit and endless

[ccp4bb] Explore Computed Structure Models Alongside PDB Data at RCSB.org | Register for Virtual Crash Course

X7NmzK556> ------ CHRISTINE ZARDECKI Deputy Director, RCSB Protein Data Bank Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 E: christine.zarde...@rcsb.org RCSB.org | facebook <https://www.facebook.com/RCSBPDB>

[ccp4bb] Applications Open for Director, RCSB Protein Data Bank

. A detailed description of the position is available <https://www.rcsb.org/pages/director-job>: https://www.rcsb.org/pages/director-job -- CHRISTINE ZARDECKI Deputy Director, RCSB Protein Data Bank Ins

[ccp4bb] Register Now for a Virtual Deep Dive into Computed Structure Model Exploration at RCSB.org

Join us as we demonstrate how RCSB.org serves as your gateway to structural data exploration on Tuesday April 30, 2024 from noon-1pm Eastern, 9-10am Pacific This event will equip you with the knowledge of how to use RCSB.org features to navigate 3D predicted protein structures in the context of